ExperimentSetReplicate

ExperimentSet4DNESCQZYHLJ
released
View JSON

in situ Hi-C on HCT-116 (HCT-116-RAD21-mAC), IAA treated to deplete Cohesin-Rad21 followed by 60 min withdrawal

   November 27th, 2018 at 6:26pm
Source Publication
The Energetics and Physiological Impact of Cohesin Extrusion.
Vian L, Pekowska A, et al., Cell 2018

Assay Description  

Note on Processed Files  

Some annotated bam and pairs files generated in this Experiment Set may contain distinct reads that share the same identifier. This was caused by merging fastq files with integer identifiers (eg. @1, @2) during processing.

Experiment Set Properties  

Set Type 
Replicate
Organism 
H. sapiens
Sample Type 
immortalized cells
Sample 
HCT116 with Crispr generated mClover and AID-tagged RAD21
Experiment Type(s) 
in situ Hi-C
Modification Type 
None
Treatment Type 
Chemical
Assay Details 
Enzyme: MboI

24 Processed Files

Quality Metrics

Experiment
For File
Filtered Reads
Cis reads (>20kb)
Short cis reads
Trans Reads
Details
From Multiple Experiments
4DNESCQZYHLJ
Multiple Experiments
File
Contact List-combined (pairs)
4DNFIMJCE95M
35.22m
54.66%
22.397%
22.943%
Experiment
4DNEXTJW44KF
Bio Rep 1, Tec Rep 1
in situ Hi-C on HCT116 with Crispr generated mClover and AID-tagged RAD21 with MboI
File
Contact List-replicate (pairs)
4DNFINWCTP8A
7.02m
55.007%
23.102%
21.891%
Experiment
4DNEXTBUGNYO
Bio Rep 2, Tec Rep 1
in situ Hi-C on HCT116 with Crispr generated mClover and AID-tagged RAD21 with MboI
File
Contact List-replicate (pairs)
4DNFIAYE3KRM
6.02m
54.609%
23.327%
22.063%
Experiment
4DNEXYORQGXF
Bio Rep 3, Tec Rep 1
in situ Hi-C on HCT116 with Crispr generated mClover and AID-tagged RAD21 with MboI
File
Contact List-replicate (pairs)
4DNFIS4DVDF9
1.42m
53.452%
19.27%
27.278%
Experiment
4DNEXHVCM2EO
Bio Rep 4, Tec Rep 1
in situ Hi-C on HCT116 with Crispr generated mClover and AID-tagged RAD21 with MboI
File
Contact List-replicate (pairs)
4DNFI67IYO67
1.63m
53.489%
20.137%
26.374%
Experiment
4DNEXA3MPMR5
Bio Rep 5, Tec Rep 1
in situ Hi-C on HCT116 with Crispr generated mClover and AID-tagged RAD21 with MboI
File
Contact List-replicate (pairs)
4DNFIMJMQDEO
2.87m
55.382%
24.237%
20.381%
Experiment
4DNEXGUER83P
Bio Rep 6, Tec Rep 1
in situ Hi-C on HCT116 with Crispr generated mClover and AID-tagged RAD21 with MboI
File
Contact List-replicate (pairs)
4DNFI5ETZUNU
3.47m
55.277%
24.546%
20.177%
Experiment
4DNEXRKOBMG5
Bio Rep 7, Tec Rep 1
in situ Hi-C on HCT116 with Crispr generated mClover and AID-tagged RAD21 with MboI
File
Contact List-replicate (pairs)
4DNFI2JSRQ1A
3.39m
56.176%
18.957%
24.867%
Experiment
4DNEXRADON17
Bio Rep 8, Tec Rep 1
in situ Hi-C on HCT116 with Crispr generated mClover and AID-tagged RAD21 with MboI
File
Contact List-replicate (pairs)
4DNFIBNICSV6
3.01m
54.963%
24.357%
20.68%
Experiment
4DNEXLR5I2I8
Bio Rep 9, Tec Rep 1
in situ Hi-C on HCT116 with Crispr generated mClover and AID-tagged RAD21 with MboI
File
Contact List-replicate (pairs)
4DNFIRA8JMU5
3.27m
53.507%
20.56%
25.934%
Experiment
4DNEXHD3YPFT
Bio Rep 10, Tec Rep 1
in situ Hi-C on HCT116 with Crispr generated mClover and AID-tagged RAD21 with MboI
File
Contact List-replicate (pairs)
4DNFIAATRXVI
3.11m
53.049%
21.308%
25.642%
Show 4 More
Experiment
For File
Failed Balancing
Details
From Multiple Experiments
4DNESCQZYHLJ
Multiple Experiments
File
Contact Matrix (mcool)
4DNFIOQLTI9G
None
Experiment
For File
Total Reads
Unmapped Reads
Multimapped Reads
Duplicate Reads
Walks
Minor Contigs
Details
Experiment
4DNEXTJW44KF
Bio Rep 1, Tec Rep 1
in situ Hi-C on HCT116 with Crispr generated mClover and AID-tagged RAD21 with MboI
File
Alignments (bam)
4DNFIXLPBKG2
9.67m
7.888%
14.244%
1.589%
3.64%
0.471%
Experiment
4DNEXTBUGNYO
Bio Rep 2, Tec Rep 1
in situ Hi-C on HCT116 with Crispr generated mClover and AID-tagged RAD21 with MboI
File
Alignments (bam)
4DNFINB11XUZ
8.26m
7.11%
14.916%
1.446%
3.65%
0.553%
Experiment
4DNEXYORQGXF
Bio Rep 3, Tec Rep 1
in situ Hi-C on HCT116 with Crispr generated mClover and AID-tagged RAD21 with MboI
File
Alignments (bam)
4DNFI1RRP2EY
1.95m
7.18%
14.572%
0.843%
4.877%
0.549%
Experiment
4DNEXHVCM2EO
Bio Rep 4, Tec Rep 1
in situ Hi-C on HCT116 with Crispr generated mClover and AID-tagged RAD21 with MboI
File
Alignments (bam)
4DNFIOTYVMY3
2.28m
7.52%
14.89%
0.832%
4.995%
0.511%
Experiment
4DNEXA3MPMR5
Bio Rep 5, Tec Rep 1
in situ Hi-C on HCT116 with Crispr generated mClover and AID-tagged RAD21 with MboI
File
Alignments (bam)
4DNFIXOICO9E
3.93m
7.186%
14.763%
1.283%
3.71%
0.43%
Experiment
4DNEXGUER83P
Bio Rep 6, Tec Rep 1
in situ Hi-C on HCT116 with Crispr generated mClover and AID-tagged RAD21 with MboI
File
Alignments (bam)
4DNFI9O4BTLW
4.73m
7.143%
14.6%
1.318%
3.631%
0.514%
Experiment
4DNEXRKOBMG5
Bio Rep 7, Tec Rep 1
in situ Hi-C on HCT116 with Crispr generated mClover and AID-tagged RAD21 with MboI
File
Alignments (bam)
4DNFI6JNCVSW
4.77m
8.438%
15.297%
0.886%
4.148%
0.359%
Experiment
4DNEXRADON17
Bio Rep 8, Tec Rep 1
in situ Hi-C on HCT116 with Crispr generated mClover and AID-tagged RAD21 with MboI
File
Alignments (bam)
4DNFI6RSRHO4
4.27m
8.388%
15.735%
0.86%
4.504%
0.55%
Experiment
4DNEXLR5I2I8
Bio Rep 9, Tec Rep 1
in situ Hi-C on HCT116 with Crispr generated mClover and AID-tagged RAD21 with MboI
File
Alignments (bam)
4DNFIQCCR861
4.38m
5.986%
13.918%
2.005%
3.415%
0.331%
Experiment
4DNEXHD3YPFT
Bio Rep 10, Tec Rep 1
in situ Hi-C on HCT116 with Crispr generated mClover and AID-tagged RAD21 with MboI
File
Alignments (bam)
4DNFIJDPQ8Q6
4.2m
5.997%
14.162%
2.046%
3.609%
0.45%